Contacts of the helix formed by residues 174 - 181 (chain A) in PDB entry 2XR9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLY 3.3 5.2 + - - +
173A PHE* 1.3 81.4 - - - +
175A ALA* 1.3 68.8 + - + +
176A SER* 3.1 20.0 + - - +
177A TYR* 3.0 41.7 + - + +
319A PRO* 3.8 23.8 - - - +
320A PHE* 3.4 24.2 - - - -
360A GLY* 4.1 7.0 - - - -
361A MET 2.7 37.6 + - - +
362A GLU* 4.3 3.8 + - - +
363A ASP* 5.5 0.2 + - - -
481A ASN* 4.9 2.3 + - - +
482A SER* 3.2 37.8 - - - +
484A GLN 3.6 7.6 - - - +
486A VAL* 4.1 0.4 - - - -
1895A IOD 3.5 25.5 - - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE 3.7 1.2 + - - -
174A ARG* 1.3 72.7 - - - +
176A SER* 1.3 60.3 + - - +
178A MET* 3.2 24.8 + - - +
179A LYS* 4.1 10.7 + - - +
199A PRO 3.8 10.2 - - - +
200A TYR* 3.7 21.5 - - + -
481A ASN 5.7 0.9 - - - +
484A GLN* 3.2 17.4 + - + +
485A THR* 3.5 17.9 - - - +
486A VAL* 3.6 11.8 - - - +
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ARG* 3.1 17.1 + - - +
175A ALA* 1.3 73.4 - - - +
177A TYR* 1.3 66.9 + - - +
178A MET 3.0 2.5 - - - -
179A LYS* 3.0 43.7 + - - +
180A LYS* 4.2 4.3 + - - +
320A PHE* 3.0 34.5 - - - -
1895A IOD 4.5 13.5 - - - -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY 3.7 10.2 + - - -
173A PHE* 3.8 15.3 - + + -
174A ARG* 3.0 46.9 + - + +
176A SER* 1.3 78.4 + - - +
178A MET* 1.3 56.8 + - - +
180A LYS* 2.9 45.9 + - - +
185A MET* 3.3 8.4 - - - +
310A PRO* 3.8 13.3 - - + +
314A GLY* 4.7 2.4 - - - -
319A PRO* 3.3 43.8 - - + +
320A PHE* 4.3 9.6 - + - -
324A MET* 3.9 17.3 - - + -
328A LEU* 3.9 29.6 - - + -
361A MET* 4.0 11.3 - - - +
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 4.1 7.8 - - + -
175A ALA 3.4 14.6 - - - +
176A SER 3.0 0.6 - - - -
177A TYR* 1.3 73.0 - - - +
179A LYS* 1.3 56.6 + - - +
180A LYS 2.9 11.0 + - - -
181A GLY* 3.3 11.1 + - - -
185A MET* 4.0 5.9 - - - +
188A ILE* 3.8 28.9 - - + -
189A GLU* 3.9 18.1 - - - +
192A ARG* 4.0 18.0 - - - -
355A PHE* 4.3 7.6 - - + -
486A VAL* 3.9 29.4 - - + -
487A PHE 5.3 0.7 - - - +
488A VAL* 3.7 30.7 - - + -
1887A IOD 4.0 23.3 - - + -
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA* 4.1 12.9 + - - +
176A SER* 3.0 43.7 + - - +
178A MET* 1.3 80.2 - - + +
180A LYS* 1.3 62.2 + - - +
181A GLY* 3.3 2.0 + - - -
199A PRO* 4.7 8.9 + - - +
200A TYR* 6.1 0.2 - - - +
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A SER 5.0 2.1 + - - +
177A TYR* 2.9 26.4 + - - +
178A MET 2.9 2.8 - - - -
179A LYS* 1.3 78.4 - - - +
181A GLY* 1.3 64.5 + - - +
183A LYS* 4.6 2.6 + - - +
184A VAL* 4.0 29.4 + - + +
185A MET* 4.4 4.5 - - + -
319A PRO 4.8 1.2 + - - -
320A PHE* 3.8 32.3 - - - +
321A GLY 5.7 1.8 - - - -
324A MET* 5.1 8.3 - - - -
325A THR* 4.3 17.7 - - - +
328A LEU* 3.5 28.5 - - + -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET 3.3 10.5 + - - -
179A LYS 3.3 4.6 - - - -
180A LYS* 1.3 78.7 - - - +
182A SER* 1.3 58.3 + - - -
183A LYS 3.2 6.9 + - - -
184A VAL* 3.3 3.3 + - - +
185A MET* 3.0 28.9 + - - +
189A GLU* 4.5 15.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il